Engineered Bacteria Manufacture and Screen Antimicrobial Peptides against Themselves

Biologists at The University of Texas at Austin have developed a method for rapidly screening hundreds of thousands of potential drugs for fighting infections, an innovation that holds promise for combating the growing scourge of antibiotic-resistant bacteria. The method involves engineering bacteria to produce and test molecules that are potentially toxic to themselves.

Lead researcher Bryan Davies, Ph.D., and colleagues say the platform, which is called SLAY (surface localized antimicrobial display), can be used to screen peptides of any length, composition, and structure. In a proof-of-concept study reported in Cell, the team used the technology to screen 800,000 random peptide molecules for antimicrobial effects. The results identified thousands of peptide sequences that were active against Escherichia coli and demonstrated different potential mechanisms of action. The team’s published paper is entitled “Discovery of Next-Generation Antimicrobials through Bacterial Self-Screening of Surface-Displayed Peptide Libraries.”

There are many platforms that can screen peptides for their ability to bind to target cells, but there are “virtually no platforms that directly assess the functionality of peptides,” the authors write. “This limitation is exacerbated when identifying antimicrobial peptides because the phenotype, death, selects against itself and has caused a scientific bottleneck that confines research to a few naturally occurring classes of antimicrobial peptides.”

The UT Austin researchers have now turned this bottleneck to their advantage and developed a method for engineering the bacteria to produce and interact with the test peptides. “We thought, wouldn’t it be great if a bacteria could synthesize the compound for us, because bacteria are cheap and easy to grow, and then test the compound on itself and report back and tell us, was that an antimicrobial or not?” says Davies, who is assistant professor of molecular biosciences.

The peptide screening technology builds on a work reported 20 years ago by UT Austin researchers, through which bacteria are induced to produce proteins or peptides on their cell surfaces. Key to the new SLAY method is the ability to genetically engineer the bacteria to produce molecules that are part test peptide and part tether. The tether anchors the complete molecule to the cell membrane, and the peptide portion is free to waft about and make contact with the bacterium’s cell surface – in much the same way that a drug molecule in the blood might interact with a pathogenic microorganism – but without interacting with other bacteria nearby.

Using this approach the team was able to create hundreds of thousands of different bacterial strains, each engineered to produce a slightly different version of a peptide molecule, and put them all into the same test tube. They used gene sequencing both at the start and at the end of the screen to find out which peptides were lethal to their host bacteria.

The study reported in Cell identified thousands of potential leads, which will need further investigation. Among the molecules identified, one, P7, was effective against other forms of pathogenic bacteria, and is safe in mice. The researchers aim to develop P7 derivatives and take them through the same screening process to identify the most effective variant.

Dr. Davies would like to see the SLAY technology become a standard tool for antibiotic drug discovery. “So what if we have a thousand groups all using this system to follow their own interests and their own peptides?” he comments. “Once you enable a community of that size, then I think you have a better chance of actually finding a new antibiotic that works.”

The UT Austin researchers have filed patent applications covering the SLAY approach and the genetic sequences of the thousands of antimicrobial peptides identified.